#!/bin/sh
#PBS -V
#PBS -j oe
#PBS -l nodes=1:ppn=1,mem=10gb,walltime=120:00:00
#PBS -q batch
Normal=$1
config_path=$2
a=$3
e=$4
#source ${config_path}/config.sh

outdir=${tree_path}/${Normal}
mkdir -p $outdir
rm -rf $outdir/*

#python3 /treeomics/src/treeomics -v ${Tree_path}/Combine_${Normal}_GGA_PASS.vcf -o ${outdir} -a ${a} -e ${e}  \
#2> ${log_path}/${Normal}_Tree.log



python /treeomics/treeomics -v ${tree_path}/Combine_${Normal}_GGA_PASS.vcf -o ${outdir} -a ${a} -e ${e}  \
2> ${log_path}/${Normal}_Tree.log


#	-e : Sequencing error rate e in the Bayesian inference model (default 1.0%)
#	-a : Maximum VAF for an absent variant fabsent before considering the estimated purity (default 5%)
#	-p : False-positive rate of conventional binary classification (only relevant for artifact comparison)
#	-i : Targeted false-discovery rate of conventional binary classification (only relevant for artifact comparison)

# sudo python3 /treeomics/src/treeomics -v ${Tree_path}/Combine_${Normal}_GGA_PASS.vcf -o ${outdir} -a 0.0001 -e 0.00001  \
# 2> ${log_path}/${Normal}_Tree.log
